DOCSLIB.ORG

Study of Actinobacteria and Their Secondary Metabolites from Various Habitats in Indonesia and Deep-Sea of the North Atlantic Ocean

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Study of Actinobacteria and Their Secondary Metabolites from Various Habitats in Indonesia and Deep-Sea of the North Atlantic Ocean Study of Actinobacteria and their Secondary Metabolites from Various Habitats in Indonesia and Deep-Sea of the North Atlantic Ocean Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Chandra Risdian aus Jakarta / Indonesien 1. Referent: Professor Dr. Michael Steinert 2. Referent: Privatdozent Dr. Joachim M. Wink eingereicht am: 18.12.2019 mündliche Prüfung (Disputation) am: 04.03.2020 Druckjahr 2020 ii Vorveröffentlichungen der Dissertation Teilergebnisse aus dieser Arbeit wurden mit Genehmigung der Fakultät für Lebenswissenschaften, vertreten durch den Mentor der Arbeit, in folgenden Beiträgen vorab veröffentlicht: Publikationen Risdian C, Primahana G, Mozef T, Dewi RT, Ratnakomala S, Lisdiyanti P, and Wink J. Screening of antimicrobial producing Actinobacteria from Enggano Island, Indonesia. AIP Conf Proc 2024(1):020039 (2018). Risdian C, Mozef T, and Wink J. Biosynthesis of polyketides in Streptomyces. Microorganisms 7(5):124 (2019) Posterbeiträge Risdian C, Mozef T, Dewi RT, Primahana G, Lisdiyanti P, Ratnakomala S, Sudarman E, Steinert M, and Wink J. Isolation, characterization, and screening of antibiotic producing Streptomyces spp. collected from soil of Enggano Island, Indonesia. The 7th HIPS Symposium, Saarbrücken, Germany (2017). Risdian C, Ratnakomala S, Lisdiyanti P, Mozef T, and Wink J. Multilocus sequence analysis of Streptomyces sp. SHP 1-2 and related species for phylogenetic and taxonomic studies. The HIPS Symposium, Saarbrücken, Germany (2019). iii Acknowledgements Acknowledgements First and foremost I would like to express my deep gratitude to my mentor PD Dr. Joachim Wink for giving me the privilege to do my PhD in his working group Microbial Strain Collection at the HZI. I thank him for his support, encouragement and guidance for carrying out my work. I would like to offer my great appreciation to Prof. Dr. Marc Stadler for his support, suggestion, and giving the opportunity to work in his laboratories in Microbial Drugs group. I also want to thank Prof. Dr. Michael Steinert for giving me opportunity as a PhD student in TU Braunschweig and becoming one of my thesis committee members. My deepest thanks to Dr. Tjandrawati Mozef as an Indonesian counterpart project leader of GINAICO (German-Indonesian Anti-Infective Cooperation). I want to thank Dr. Puspita Lisdiyanti, Dr. Shanti Ratnakomala, and Dr. Rizna Triana Dewi and all of my Indonesian collaboration partners from Research Center for Chemistry and Research Center for Biotechnology LIPI. I would like to give special thanks to the DAAD (Deutscher Akademischer Austauschdienst) for the financial support and assistance during my PhD studies, and to German Federal Ministry of Education and Research (BMBF) under the GINAICO project, the President’s Initiative and Networking Funds of the Helmholtz Association of German Research Centres under Contract Number VHGS-202, and Ministry of Research, Technology and Higher Education of the Republic of Indonesia (RISTEKDIKTI) for supporting my PhD project. I extend my gratitudes to my collaboration partners Prof. Dr. Eike Steinmann, Dr. Kathrin Mohr, Dr. Sabrina Karwehl, Dr. Enge Sudarman, Dr. Rolf Jansen, Dr. Manfred Rohde, Dr. Richard Hahnke, Dr. Peter Schumann, Dr. Cathrin Spröer, Dr. Boyke Bunk, and Gabriele Pötter. I would like to thank members of the working groups Microbial Strain Collection especially Christiane Fritz-Braun, Kerstin Schober, Silke Reinecke, Axel Schulz and Tian Cheng for the great support during my PhD work. I want to thank Gian Primahana, Senlie Octaviana, Zahra Noviana, and Dimas F. Praditya for helping me in chemistry part, Actinobacteria isolation, DNA analysis, and antiviral assay, and TU iv Acknowledgements Braunschweig students from IB20B practical group. My deepest thanks to Romy Schade, Aileen Gollasch, Klaus Peter Conrad, Stephanie Schulz, Birte Trunkwalter, Wera Collisi, Jolanta Lulla, Hannes Meyer for the best technical support. I thank all of my other colleagues in the Microbial Strain Collection at the HZI for the good work environment: Dr. Lucky Mulwa, Rina Andriyani, Shadi Khodamoradi, and Nasim Safaei. Lastly, I would like to dedicate this work to my family for their love and support throughout the years, especially to my wife Yayu Sri Rahayu and my children Nashwa Levareyna Risdian and Naufal Zeinizar Risdian. v Table of Contents Table of Contents Acknowledgements ..................................................................................................... iv Table of Contents ........................................................................................................ vi List of Figures ............................................................................................................. ix List of Tables .............................................................................................................. xi List of Abbreviations ................................................................................................. xii Abstract ..................................................................................................................... xiii Abstrakt ..................................................................................................................... xiv 1 Introduction ............................................................................................... 1 1.1 Natural product and drug discovery .......................................................... 1 1.2 Actinobacteria ........................................................................................... 5 1.2.1 Streptomyces ............................................................................................. 7 1.2.2 Non-Streptomyces Actinobacteria ............................................................. 9 1.3 Polyphasic taxonomy of the class Actinobacteria ................................... 11 1.3.1 Phenotypic analysis ................................................................................. 14 1.3.2 Genomic and phylogenetic analysis ........................................................ 16 1.4 Dereplication and isolation of natural products from Actinobacteria ..... 18 1.5 Hepatitis .................................................................................................. 19 1.6 Previous work ......................................................................................... 20 1.7 Aim of study............................................................................................ 20 2 Materials and Methods ............................................................................ 21 2.1 Materials.................................................................................................. 21 2.1.1 Media ...................................................................................................... 21 2.1.2 Chemicals ................................................................................................ 25 2.1.3 Source of samples ................................................................................... 27 2.1.4 Organisms ............................................................................................... 30 2.1.5 Kits and enzymes .................................................................................... 32 2.1.6 Primers .................................................................................................... 32 2.1.7 Equipment ............................................................................................... 34 2.2 Methods ................................................................................................... 35 2.2.1 Sampling ................................................................................................. 35 2.2.2 Isolation of Actinobacteria ...................................................................... 35 2.2.3 Extract Production................................................................................... 35 2.2.4 Analysis of 16S rRNA sequences ........................................................... 36 vi Table of Contents 2.2.5 Morphology and melanin production ...................................................... 37 2.2.6 Physiological and biochemical characteristic ......................................... 37 2.2.6.1 Growth at different temperature and pH ....................................... 37 2.2.6.2 Carbon utilization ......................................................................... 38 2.2.6.3 Sodium chloride tolerance ............................................................ 38 2.2.6.4 Enzymatic assay ............................................................................ 38 2.2.6.5 Antibiotic susceptibility ................................................................ 39 2.2.7 Chemotaxonomy ..................................................................................... 39 2.2.7.1 Freeze-dried cells preparation ....................................................... 39 2.2.7.2 Cell wall amino acid analysis ....................................................... 39 2.2.7.3 Whole-cell sugar analysis ............................................................. 40 2.2.7.4 Menaquinone analysis................................................................... 40 2.2.7.5 Polar lipid analysis ........................................................................ 41 2.2.7.6
Load more

Recommended publications
  • Identification and Antibiosis of a Novel Actinomycete Strain RAF-11 Isolated from Iraqi Soil
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by GSSRR.ORG: International Journals: Publishing Research Papers in all Fields International Journal of Sciences: Basic and Applied Research (IJSBAR) ISSN 2307-4531 http://gssrr.org/index.php?journal=JournalOfBasicAndApplied Identification and Antibiosis of a Novel Actinomycete Strain RAF-11 Isolated From Iraqi Soil. R. FORAR. LAIDIa, A. ABDERRAHMANEb, A. A. HOCINE NORYAc. a Department of Natural Sciences, Ecole Normale Superieure, Vieux-Kouba, Algiers – Algeria b,c Institute of Genetic Engineering and Biotechnology, Baghdad - Iraq. a email: [email protected] Abstract A total of 35 actinomycetes strains were isolated from and around Baghdad, Iraq, at a depth of 5-10 m, by serial dilution agar plating method. Nineteen out of them showed noticeable antimicrobial activities against at least, to one of the target pathogens. Five among the nineteen were active against both Gram positive and Gram negative bacteria, yeasts and moulds. The most active isolate, strain RAF-11, based on its largest zone of inhibition and strong antifungal activity, especially against Candida albicans and Aspergillus niger, the causative of candidiasis and aspergillosis respectively, was selected for identification. Morphological and chemical studies indicated that this isolate belongs to the genus Streptomyces. Analysis of the 16S rDNA sequence showed a high similarity, 98 %, with the most closely related species, Streptomyces labedae NBRC 15864T/AB184704, S. erythrogriseus LMG 19406T/AJ781328, S. griseoincarnatus LMG 19316T/AJ781321 and S. variabilis NBRC 12825T/AB184884, having the closest match. From the taxonomic features, strain RAF-11 matched with S. labedae, in the morphological, physiological and biochemical characters, however it showed significant differences in morphological characteristics with this nearest species, S.
    [Show full text]
  • Estimation of Antimicrobial Activities and Fatty Acid Composition Of
    Estimation of antimicrobial activities and fatty acid composition of actinobacteria isolated from water surface of underground lakes from Badzheyskaya and Okhotnichya caves in Siberia Irina V. Voytsekhovskaya1,*, Denis V. Axenov-Gribanov1,2,*, Svetlana A. Murzina3, Svetlana N. Pekkoeva3, Eugeniy S. Protasov1, Stanislav V. Gamaiunov2 and Maxim A. Timofeyev1 1 Irkutsk State University, Irkutsk, Russia 2 Baikal Research Centre, Irkutsk, Russia 3 Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences, Petrozavodsk, Karelia, Russia * These authors contributed equally to this work. ABSTRACT Extreme and unusual ecosystems such as isolated ancient caves are considered as potential tools for the discovery of novel natural products with biological activities. Acti- nobacteria that inhabit these unusual ecosystems are examined as a promising source for the development of new drugs. In this study we focused on the preliminary estimation of fatty acid composition and antibacterial properties of culturable actinobacteria isolated from water surface of underground lakes located in Badzheyskaya and Okhotnichya caves in Siberia. Here we present isolation of 17 strains of actinobacteria that belong to the Streptomyces, Nocardia and Nocardiopsis genera. Using assays for antibacterial and antifungal activities, we found that a number of strains belonging to the genus Streptomyces isolated from Badzheyskaya cave demonstrated inhibition activity against Submitted 23 May 2018 bacteria and fungi. It was shown that representatives of the genera Nocardia and Accepted 24 September 2018 Nocardiopsis isolated from Okhotnichya cave did not demonstrate any tested antibiotic Published 25 October 2018 properties. However, despite the lack of antimicrobial and fungicidal activity of Corresponding author Nocardia extracts, those strains are specific in terms of their fatty acid spectrum.
    [Show full text]
  • Alpine Soil Bacterial Community and Environmental Filters Bahar Shahnavaz
    Alpine soil bacterial community and environmental filters Bahar Shahnavaz To cite this version: Bahar Shahnavaz. Alpine soil bacterial community and environmental filters. Other [q-bio.OT]. Université Joseph-Fourier - Grenoble I, 2009. English. tel-00515414 HAL Id: tel-00515414 https://tel.archives-ouvertes.fr/tel-00515414 Submitted on 6 Sep 2010 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE Pour l’obtention du titre de l'Université Joseph-Fourier - Grenoble 1 École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Par Bahar SHAHNAVAZ Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. Thierry HEULIN Rapporteur Dr. Christian JEANTHON Rapporteur Dr. Sylvie NAZARET Examinateur Dr. Jean MARTIN Examinateur Dr. Yves JOUANNEAU Président du jury Dr. Roberto GEREMIA Directeur de thèse Thèse préparée au sien du Laboratoire d’Ecologie Alpine (LECA, UMR UJF- CNRS 5553) THÈSE Pour l’obtention du titre de Docteur de l’Université de Grenoble École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Bahar SHAHNAVAZ Directeur : Roberto GEREMIA Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr.
    [Show full text]
  • Genomic and Phylogenomic Insights Into the Family Streptomycetaceae Lead
    1 Supplementary Material 2 Genomic and phylogenomic insights into the family Streptomycetaceae lead 3 to proposal of Charcoactinosporaceae fam. nov. and 8 novel genera with 4 emended descriptions of Streptomyces calvus 5 Munusamy Madhaiyan1, †, *, Venkatakrishnan Sivaraj Saravanan2, †, Wah-Seng See-Too3, † 6 1Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 7 Singapore 117604; 2Department of Microbiology, Indira Gandhi College of Arts and Science, 8 Kathirkamam 605009, Pondicherry, India; 3Division of Genetics and Molecular Biology, 9 Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 10 Malaysia 1 11 Table S3. List of the core genes in the genome used for phylogenomic analysis. NCBI Protein Accession Gene WP_074993204.1 NUDIX hydrolase WP_070028582.1 YggS family pyridoxal phosphate-dependent enzyme WP_074992763.1 ParB/RepB/Spo0J family partition protein WP_070022023.1 lipoyl(octanoyl) transferase LipB WP_070025151.1 FABP family protein WP_070027039.1 heat-inducible transcriptional repressor HrcA WP_074992865.1 folate-binding protein YgfZ WP_074992658.1 recombination protein RecR WP_074991826.1 HIT domain-containing protein WP_070024163.1 adenylosuccinate synthase WP_009190566.1 anti-sigma regulatory factor WP_071828679.1 preprotein translocase subunit SecG WP_070026304.1 50S ribosomal protein L13 WP_009190144.1 30S ribosomal protein S5 WP_014674378.1 30S ribosomal protein S8 WP_070026314.1 50S ribosomal protein L5 WP_009300593.1 30S ribosomal protein S13 WP_003998809.1
    [Show full text]
  • Improved Taxonomy of the Genus Streptomyces
    UNIVERSITEIT GENT Faculteit Wetenschappen Vakgroep Biochemie, Fysiologie & Microbiologie Laboratorium voor Microbiologie Improved taxonomy of the genus Streptomyces Benjamin LANOOT Scriptie voorgelegd tot het behalen van de graad van Doctor in de Wetenschappen (Biochemie) Promotor: Prof. Dr. ir. J. Swings Co-promotor: Dr. M. Vancanneyt Academiejaar 2004-2005 FACULTY OF SCIENCES ____________________________________________________________ DEPARTMENT OF BIOCHEMISTRY, PHYSIOLOGY AND MICROBIOLOGY UNIVERSITEIT LABORATORY OF MICROBIOLOGY GENT IMPROVED TAXONOMY OF THE GENUS STREPTOMYCES DISSERTATION Submitted in fulfilment of the requirements for the degree of Doctor (Ph D) in Sciences, Biochemistry December 2004 Benjamin LANOOT Promotor: Prof. Dr. ir. J. SWINGS Co-promotor: Dr. M. VANCANNEYT 1: Aerial mycelium of a Streptomyces sp. © Michel Cavatta, Academy de Lyon, France 1 2 2: Streptomyces coelicolor colonies © John Innes Centre 3: Blue haloes surrounding Streptomyces coelicolor colonies are secreted 3 4 actinorhodin (an antibiotic) © John Innes Centre 4: Antibiotic droplet secreted by Streptomyces coelicolor © John Innes Centre PhD thesis, Faculty of Sciences, Ghent University, Ghent, Belgium. Publicly defended in Ghent, December 9th, 2004. Examination Commission PROF. DR. J. VAN BEEUMEN (ACTING CHAIRMAN) Faculty of Sciences, University of Ghent PROF. DR. IR. J. SWINGS (PROMOTOR) Faculty of Sciences, University of Ghent DR. M. VANCANNEYT (CO-PROMOTOR) Faculty of Sciences, University of Ghent PROF. DR. M. GOODFELLOW Department of Agricultural & Environmental Science University of Newcastle, UK PROF. Z. LIU Institute of Microbiology Chinese Academy of Sciences, Beijing, P.R. China DR. D. LABEDA United States Department of Agriculture National Center for Agricultural Utilization Research Peoria, IL, USA PROF. DR. R.M. KROPPENSTEDT Deutsche Sammlung von Mikroorganismen & Zellkulturen (DSMZ) Braunschweig, Germany DR.
    [Show full text]
  • Biological and Chemical Diversity of Bacteria Associated with a Marine Flatworm
    Article Biological and Chemical Diversity of Bacteria Associated with a Marine Flatworm Hui-Na Lin 1,2,†, Kai-Ling Wang 1,3,†, Ze-Hong Wu 4,5, Ren-Mao Tian 6, Guo-Zhu Liu 7 and Ying Xu 1,* 1 Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; [email protected] (H.-N.L.); [email protected] (K.-L.W.) 2 School of Life Sciences, Xiamen University, Xiamen 361102, China 3 Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China 4 The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China; [email protected] 5 Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou 510632, China 6 Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China; [email protected] 7 HEC Research and Development Center, HEC Pharm Group, Dongguan 523871, China; [email protected] * Correspondence: [email protected]; Tel.: +86-755-26958849; Fax: +86-755-26534274 † These authors contributed equally to this work. Received: 20 July 2017; Accepted: 29 August 2017; Published: 1 September 2017 Abstract: The aim of this research is to explore the biological and chemical diversity of bacteria associated with a marine flatworm Paraplanocera sp., and to discover the bioactive metabolites from culturable strains. A total of 141 strains of bacteria including 45 strains of actinomycetes and 96 strains of other bacteria were isolated, identified and fermented on a small scale.
    [Show full text]
  • A Novel Hydroxamic Acid-Containing Antibiotic Produced by a Saharan Soil-Living Streptomyces Strain A
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Open Archive Toulouse Archive Ouverte . . . . A novel hydroxamic acid-containing antibiotic produced by Streptomyces a Saharan soil-living strain 1,2 1 3 1 4 4 5 1 A. Yekkour , A. Meklat , C. Bijani , O. Toumatia , R. Errakhi , A. Lebrihi , F. Mathieu , A. Zitouni 1 and N. Sabaou 1 Laboratoire de Biologie des Systemes Microbiens (LBSM), Ecole Normale Superieure de Kouba, Alger, Algeria 2 Centre de Recherche Polyvalent, Institut National de la Recherche Agronomique d’Algerie, Alger, Algeria 3 Laboratoire de Chimie de Coordination (LCC), CNRS, Universite de Toulouse, UPS, INPT, Toulouse, France 4 Universite Moulay Ismail, Meknes, Morocco 5 Universite de Toulouse, Laboratoire de Genie Chimique UMR 5503 (CNRS/INPT/UPS), INP de Toulouse/ENSAT, Castanet-Tolosan Cedex, France Significance and Impact of the Study: This study presents the isolation of a Streptomyces strain, named WAB9, from a Saharan soil in Algeria. This strain was found to produce a new hydroxamic acid-contain- ing molecule with interesting antimicrobial activities towards various multidrug-resistant micro-organ- isms. Although hydroxamic acid-containing molecules are known to exhibit low toxicities in general, only real evaluations of the toxicity levels could decide on the applications for which this new molecule is potentially most appropriate. Thus, this article provides a new framework of research. Keywords Abstract antimicrobial activity, hydroxamic acid, Streptomyces, structure elucidation, During screening for potentially antimicrobial actinobacteria, a highly taxonomy. antagonistic strain, designated WAB9, was isolated from a Saharan soil of Algeria. A polyphasic approach characterized the strain taxonomically as a Correspondence member of the genus Streptomyces.
    [Show full text]
  • Diversity of Free-Living Nitrogen Fixing Bacteria in the Badlands of South Dakota Bibha Dahal South Dakota State University
    South Dakota State University Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange Theses and Dissertations 2016 Diversity of Free-living Nitrogen Fixing Bacteria in the Badlands of South Dakota Bibha Dahal South Dakota State University Follow this and additional works at: http://openprairie.sdstate.edu/etd Part of the Bacteriology Commons, and the Environmental Microbiology and Microbial Ecology Commons Recommended Citation Dahal, Bibha, "Diversity of Free-living Nitrogen Fixing Bacteria in the Badlands of South Dakota" (2016). Theses and Dissertations. 688. http://openprairie.sdstate.edu/etd/688 This Thesis - Open Access is brought to you for free and open access by Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. For more information, please contact [email protected]. DIVERSITY OF FREE-LIVING NITROGEN FIXING BACTERIA IN THE BADLANDS OF SOUTH DAKOTA BY BIBHA DAHAL A thesis submitted in partial fulfillment of the requirements for the Master of Science Major in Biological Sciences Specialization in Microbiology South Dakota State University 2016 iii ACKNOWLEDGEMENTS “Always aim for the moon, even if you miss, you’ll land among the stars”.- W. Clement Stone I would like to express my profuse gratitude and heartfelt appreciation to my advisor Dr. Volker Brӧzel for providing me a rewarding place to foster my career as a scientist. I am thankful for his implicit encouragement, guidance, and support throughout my research. This research would not be successful without his guidance and inspiration.
    [Show full text]
  • Isolation and Characterisation of Metal- Tolerant Actinomycetes from a Karstic Cave in Malaysia
    ISOLATION AND CHARACTERISATION OF METAL- TOLERANT ACTINOMYCETES FROM A KARSTIC CAVE IN MALAYSIA YAP SIEW MEI INSTITUTE OF BIOLOGICAL SCIENCES FACULTY OF SCIENCE UNIVERSITY OF MALAYA KUALA LUMPUR 2015 ISOLATION AND CHARACTERISATION OF METAL-TOLERANT ACTINOMYCETES FROM A KARSTIC CAVE IN MALAYSIA YAP SIEW MEI DISSERTATION SUBMITTED IN FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE INSTITUTE OF BIOLOGICAL SCIENCES FACULTY OF SCIENCE UNIVERSITY OF MALAYA KUALA LUMPUR 2015 UNIVERSITI MALAYA ORIGINAL LITERARY WORK DECLARATION Name of Candidate: YAP SIEW MEI I/C/Passport No: 860125-14-5378 Regisration/Matric No.: SGR080119 Name of Degree: MASTER OF SCIENCE Title of Project Paper/Research Report/Dissertation/Thesis (“this Work”): “ISOLATION AND CHARACTERISATION OF METAL-TOLERANT ACTINOMYCETES FROM A KARSTIC CAVE IN MALAYSIA” Field of Study: ENVIRONMENTAL MICROBIOLOGY I do solemnly and sincerely declare that: (1) I am the sole author/writer of this Work, (2) This Work is original, (3) Any use of any work in which copyright exists was done by way of fair dealing and for permitted purposes and any excerpt or extract from, or reference to or reproduction of any copyright work has been disclosed expressly and sufficiently and the title of the Work and its authorship have been acknowledged in this Work, (4) I do not have any actual knowledge nor do I ought reasonably to know that the making of this work constitutes an infringement of any copyright work, (5) I hereby assign all and every rights in the copyright to this Work to the University of Malaya (“UM”), who henceforth shall be owner of the copyright in this Work and that any reproduction or use in any form or by any means whatsoever is prohibited without the written consent of UM having been first had and obtained, (6) I am fully aware that if in the course of making this Work I have infringed any copyright whether intentionally or otherwise, I may be subject to legal action or any other action as may be determined by UM.
    [Show full text]
  • The Degradative Capabilities of New Amycolatopsis Isolates on Polylactic Acid
    microorganisms Article The Degradative Capabilities of New Amycolatopsis Isolates on Polylactic Acid Francesca Decorosi 1,2, Maria Luna Exana 1,2, Francesco Pini 1,2, Alessandra Adessi 1 , Anna Messini 1, Luciana Giovannetti 1,2 and Carlo Viti 1,2,* 1 Department of Agriculture, Food, Environment and Forestry (DAGRI)—University of Florence, Piazzale delle Cascine 18, I50144 Florence, Italy; francesca.decorosi@unifi.it (F.D.); [email protected] (M.L.E.); francesco.pini@unifi.it (F.P.); alessandra.adessi@unifi.it (A.A.); anna.messini@unifi.it (A.M.); luciana.giovannetti@unifi.it (L.G.) 2 Genexpress Laboratory, Department of Agriculture, Food, Environment and Forestry (DAGRI)—University of Florence, Via della Lastruccia 14, I50019 Sesto Fiorentino, Italy * Correspondence: carlo.viti@unifi.it; Tel.: +39-05-5457-3224 Received: 15 October 2019; Accepted: 18 November 2019; Published: 20 November 2019 Abstract: Polylactic acid (PLA), a bioplastic synthesized from lactic acid, has a broad range of applications owing to its excellent proprieties such as a high melting point, good mechanical strength, transparency, and ease of fabrication. However, the safe disposal of PLA is an emerging environmental problem: it resists microbial attack in environmental conditions, and the frequency of PLA-degrading microorganisms in soil is very low. To date, a limited number of PLA-degrading bacteria have been isolated, and most are actinomycetes. In this work, a method for the selection of rare actinomycetes with extracellular proteolytic activity was established, and the technique was used to isolate four mesophilic actinomycetes with the ability to degrade emulsified PLA in agar plates. All four strains—designated SO1.1, SO1.2, SNC, and SST—belong to the genus Amycolatopsis.
    [Show full text]
  • Genomic and Phylogenomic Insights Into the Family Streptomycetaceae Lead to Proposal of Charcoactinosporaceae Fam. Nov. and 8 No
    bioRxiv preprint doi: https://doi.org/10.1101/2020.07.08.193797; this version posted July 8, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Genomic and phylogenomic insights into the family Streptomycetaceae 2 lead to proposal of Charcoactinosporaceae fam. nov. and 8 novel genera 3 with emended descriptions of Streptomyces calvus 4 Munusamy Madhaiyan1, †, * Venkatakrishnan Sivaraj Saravanan2, † Wah-Seng See-Too3, † 5 1Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 6 Singapore 117604; 2Department of Microbiology, Indira Gandhi College of Arts and Science, 7 Kathirkamam 605009, Pondicherry, India; 3Division of Genetics and Molecular Biology, 8 Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 9 Malaysia 10 *Corresponding author: Temasek Life Sciences Laboratory, 1 Research Link, National 11 University of Singapore, Singapore 117604; E-mail: [email protected] 12 †All these authors have contributed equally to this work 13 Abstract 14 Streptomycetaceae is one of the oldest families within phylum Actinobacteria and it is large and 15 diverse in terms of number of described taxa. The members of the family are known for their 16 ability to produce medically important secondary metabolites and antibiotics. In this study, 17 strains showing low 16S rRNA gene similarity (<97.3 %) with other members of 18 Streptomycetaceae were identified and subjected to phylogenomic analysis using 33 orthologous 19 gene clusters (OGC) for accurate taxonomic reassignment resulted in identification of eight 20 distinct and deeply branching clades, further average amino acid identity (AAI) analysis showed 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.08.193797; this version posted July 8, 2020.
    [Show full text]
  • Actinomycetes Isolated from Wetland and Hill Paddy During the Warm and Cool Seasons in Sarawak, East Malaysia
    ACTINOMYCETES ISOLATED FROM WETLAND AND HILL PADDY DURING THE WARM AND COOL SEASONS IN SARAWAK, EAST MALAYSIA Ann Anni Basik*, Holed Juboi, Sunita Sara Gill Shamsul, Jean-Jacques Sanglier and Tiong Chia Yeo Address(es): Ann Anni Basik 1 Sarawak Biodiversity Centre, Km. 20 Jalan Borneo Heights, Semengoh, 93250 Kuching, Sarawak, Malaysia. *Corresponding author: [email protected] doi: 10.15414/jmbfs.2020.9.4.774-780 ARTICLE INFO ABSTRACT Received 12. 3. 2018 As part of the Natural Product Discovery programme at Sarawak Biodiversity Centre (SBC), our study targeted isolation and evaluation Revised 4. 9. 2019 of actinomycetes diversity from paddy rice fields. Samples from two types of paddy farming system practiced in Sarawak, wet land and Accepted 11. 9. 2019 hill paddy, were collected and processed leading to the selection of 578 strains distributed among 24 genera and 10 families. Analysis Published 3. 2. 2020 using phylogenetic clustering indicated a total of 159 taxonomic units (TU). The taxonomic position and the ranking of the TU allowed their classification in 4 novel species, 61 putative novel species and 94 known species or species of uncertain position. The high genus diversity and percentage of novel or putative novel species demonstrate the biodiversity potential of Sarawak ecosystems, even in man- Regular article managed ecosystems. Keywords: paddy field, actinomycetes, ranking, taxonomic unit INTRODUCTION sequence identity (Gevers et al., 2005). However, species can be differentiated at a level of 98.2 – 99 % 16S rRNA similarity (Kim et al., 2014). Isolation of rare actinomycetes from paddy rice (Oryza sativa L.) field in the Apart from the commonly collected soil samples, rhizospheric soil and roots were Kuching Division, Sarawak were made to evaluate their diversity and also included for the isolation of actinomycetes in this project.
    [Show full text]